Journal of Biomolecular Structure & Dynamics最新文献_第6页

Salp-J Colony Optimization-based advanced hybrid ensemble deep predictor with LSTM for protein structure prediction. 基于 Salp-J 殖民地优化的高级混合集合深度预测器与 LSTM 用于蛋白质结构预测。

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-04-01 Epub Date: 2024-03-06 DOI: 10.1080/07391102.2023.2294386

Swati Jadhav, Arati J Vyavahare, Manish Sharma

{"title":"Salp-J Colony Optimization-based advanced hybrid ensemble deep predictor with LSTM for protein structure prediction.","authors":"Swati Jadhav, Arati J Vyavahare, Manish Sharma","doi":"10.1080/07391102.2023.2294386","DOIUrl":"10.1080/07391102.2023.2294386","url":null,"abstract":"Protein structure prediction (PSP) is a key concern in computational biology, which is considered a challenging task that is vital to determine the structure and the protein function since each protein possesses a definite shape, whereas the protein secondary structure prediction (PSSP) is the foundation for three-dimensional PSP. An Advanced hybrid ensemble deep predictor is utilized for predicting the structure of a protein using Long-Short Term Memory (LSTM), in which the performance of the predictor is improved for obtaining the features through the Salp-J Colony Optimization, which is developed by integrating the features of three optimizations the exploration behavior of Ulmaris, the immune system of virus colony and the teamwork of salp for solution update that helps to predict the accurate protein structure. The proposed method achieved the value of 99.1% accuracy, 99.5% sensitivity, 98.85% specificity, and 0.9% error at the 80% of training percentage 90 using CullPDB. Similarly, in Protein Net, the attained value of accuracy is 97.27%, sensitivity is 98.13%, specificity is 97%, and error is 2.7% concerning training percentage 90%.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"2901-2916"},"PeriodicalIF":2.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140039408","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Exploring the hub genes and potential drugs involved in Fanconi anemia using microarray datasets and bioinformatics analysis. 利用微阵列数据集和生物信息学分析，探索范可尼贫血症的中心基因和潜在药物。

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-04-01 Epub Date: 2023-12-27 DOI: 10.1080/07391102.2023.2297008

Alaa R Hameed, Sama Fakhri Ali, Taghreed N Almanaa, Mohammad Abdullah Aljasir, Abdulmohsen M Alruwetei, Samira Sanami, Hassan Ayaz, Ijaz Ali, Faisal Ahmad, Sajjad Ahmad

{"title":"Exploring the hub genes and potential drugs involved in Fanconi anemia using microarray datasets and bioinformatics analysis.","authors":"Alaa R Hameed, Sama Fakhri Ali, Taghreed N Almanaa, Mohammad Abdullah Aljasir, Abdulmohsen M Alruwetei, Samira Sanami, Hassan Ayaz, Ijaz Ali, Faisal Ahmad, Sajjad Ahmad","doi":"10.1080/07391102.2023.2297008","DOIUrl":"10.1080/07391102.2023.2297008","url":null,"abstract":"Fanconi anemia (FA) is a genetic disorder that occurs when certain genes responsible for repairing DNA replication and promoting homologous recombination fail to function properly. This leads to severe clinical symptoms and a wide range of cancer-related characteristics. Recent treatment approaches for FA involve hematopoietic stem cell transplantation (HSCT), which helps restore the population of stem cells. A survival study using p-values indicated that specific hub genes play a significant role in diagnosing and predicting the disease. To find potential medications that interact with the identified hub genes, researchers inferred drugs. Among hub genes, TP53 was found to be particularly promising through computational analysis. Further investigation focused on two drugs, Topiramate and Tocofersolan predicted based on drug bank database analysis. Molecular docking strategies were employed to assess the best binding pose of these drugs with TP53. Topiramate showed a binding affinity of -6.5 kcal/mol, while Tocofersolan showed -8.5 kcal/mol against the active residues within the binding pocket. Molecular dynamics (MD) simulations were conducted to observe the stability of each drug's interaction with the TP53 protein over time. Both drugs exhibited stable confirmation with only slight changes in the loop region of the TP53 protein during the simulation intervals. Results also shows that there was a high fluctuation observed during apo-sate simulation time intervals as compared to complex system. Hence, it is suggested that the exploration of structure-based drug design holds promising results to specific target. This could potentially lead to a breakthrough in future experimental approaches for FA treatment.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"3297-3310"},"PeriodicalIF":2.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139040038","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Unleashing the binding interaction of chrysin-Cu(II) complex with the biomacromolecular targets: further studies of cell cytotoxicity and radical scavenging properties. 释放金丝桃素-Cu(II)复合物与生物大分子目标的结合相互作用：细胞毒性和自由基清除特性的进一步研究。

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-04-01 Epub Date: 2024-01-08 DOI: 10.1080/07391102.2023.2300122

Sharat Sarmah, Ibemhanbi Konthoujam, Vivek Prakash, Kripamoy Aguan, Atanu Singha Roy

{"title":"Unleashing the binding interaction of chrysin-Cu(II) complex with the biomacromolecular targets: further studies of cell cytotoxicity and radical scavenging properties.","authors":"Sharat Sarmah, Ibemhanbi Konthoujam, Vivek Prakash, Kripamoy Aguan, Atanu Singha Roy","doi":"10.1080/07391102.2023.2300122","DOIUrl":"10.1080/07391102.2023.2300122","url":null,"abstract":"Flavonoids are significant dietary components and have ability to coordinate with metal ions to produce novel drug discovery leads that are superior to those of the parent flavonoids. Here, in this report, we have synthesized chrysin-Cu(II) complex (as per reported article) and characterized it further with different analytical techniques. The synthesized complex was evaluated for radical scavenging and cell cytotoxicity studies where it exhibited enhanced activity as compared to bare chrysin. The interaction studies of the complex with ct-DNA (Kb ⁓ 105 M-1), human serum albumin (HSA) and ovalbumin (Kb ⁓ 104 M-1) were evaluated using multi-spectroscopic and molecular docking studies. Groove binding mode with ct-DNA was observed as confirmed from competitive displacement studies, viscosity measurement, melting temperature estimation and docking analyses. The complex exhibited comparatively higher affinity towards ct-DNA which indicated it efficient transportation by the carrier proteins and controlled release in the target DNA.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"3671-3687"},"PeriodicalIF":2.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139377691","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Biological evaluations and computational studies of newly synthesized thymol-based Schiff bases as anticancer, antimicrobial and antioxidant agents. 对新合成的以百里酚为基础的希夫碱作为抗癌、抗菌和抗氧化剂进行生物学评估和计算研究。

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-04-01 Epub Date: 2023-12-26 DOI: 10.1080/07391102.2023.2297813

Dicle Sahin, Remziye Aysun Kepekci, Burçin Türkmenoğlu, Senem Akkoc

{"title":"Biological evaluations and computational studies of newly synthesized thymol-based Schiff bases as anticancer, antimicrobial and antioxidant agents.","authors":"Dicle Sahin, Remziye Aysun Kepekci, Burçin Türkmenoğlu, Senem Akkoc","doi":"10.1080/07391102.2023.2297813","DOIUrl":"10.1080/07391102.2023.2297813","url":null,"abstract":"Three new thymol-based molecules were synthesized and evaluated as anticancer, antimicrobial and antioxidant agents. Liver, colon, lung and prostate cancer cell lines were utilized in cytotoxicity tests. The results demonstrated that synthesized molecules had a cytotoxic effect against the screened cell lines. One of the molecules (4a) was found to have a higher efficacy towards the colon cancer cell line (DLD-1) with an IC50 value of 12.39 µM and the other (4c) towards the prostate cancer cell line (PC3) with an IC50 value of 7.67 µM than the positive control drug cisplatin. To assess the antimicrobial activity of molecules (4a-c), Gram-positive bacteria, Gram-negative bacteria and yeast were subjected to agar disc diffusion and broth microdilution assays. The investigation of antioxidant potential was conducted using the DPPH radical scavenging activity assay. While all compounds displayed strong cytotoxic and antioxidant properties, they exhibited only moderate antimicrobial activity. Molecular docking studies were performed on epidermal growth factor receptor (EGFR), vascular endothelial growth factor receptor 2 (VEGFR-2), focal adhesion kinase (FAK), B-Raf and phosphoinositide 3-kinase (PI3K). The binding energies and interactions obtained from the docking results of compounds (4a-c) supported the experimental results. Drug similarity rates and pharmacokinetic properties were analyzed with the absorption, distribution, metabolism and excretion (ADME) method. Geometric parameters such as chemical potential (µ), electrophilicity index (ω) and chemical softness (σ) of compounds (4a-c) were calculated using the 6-31*G basis set B3LYP method.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"3375-3389"},"PeriodicalIF":2.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139040037","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Combining QSAR techniques, molecular docking, and molecular dynamics simulations to explore anti-tumor inhibitors targeting Focal Adhesion Kinase. 结合 QSAR 技术、分子对接和分子动力学模拟，探索针对 Focal Adhesion Kinase 的抗肿瘤抑制剂。

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-04-01 Epub Date: 2024-01-03 DOI: 10.1080/07391102.2023.2301055

Yuan Liu, Jian-Bo Tong, Peng Gao, Xuan-Lu Fan, Xue-Chun Xiao, Yi-Chaung Xing

{"title":"Combining QSAR techniques, molecular docking, and molecular dynamics simulations to explore anti-tumor inhibitors targeting Focal Adhesion Kinase.","authors":"Yuan Liu, Jian-Bo Tong, Peng Gao, Xuan-Lu Fan, Xue-Chun Xiao, Yi-Chaung Xing","doi":"10.1080/07391102.2023.2301055","DOIUrl":"10.1080/07391102.2023.2301055","url":null,"abstract":"Focal Adhesion Kinase (FAK) is an important target for tumor therapy and is closely related to tumor cell genesis and progression. In this paper, we selected 46 FAK inhibitors with anticancer activity in the pyrrolo pyrimidine backbone to establish 3D/2D-QSAR models to explore the relationship between inhibitory activity and molecular structure. We have established two ideal models, namely, the Topomer CoMFA model (<math><mrow><msup><mrow><mi>q</mi></mrow><mrow><mn>2</mn></mrow></msup></mrow></math>= 0.715, <math><mrow><msup><mrow><mi>r</mi></mrow><mrow><mn>2</mn></mrow></msup></mrow></math>= 0.984) and the Holographic Quantitative Structure-Activity Relationship (HQSAR) model (<math><mrow><msup><mrow><mi>q</mi></mrow><mrow><mn>2</mn></mrow></msup></mrow></math>= 0.707, <math><mrow><msup><mrow><mi>r</mi></mrow><mrow><mn>2</mn></mrow></msup></mrow></math>= 0.899). Both models demonstrate excellent external prediction capabilities.Based on the QSAR results, we designed 20 structurally modified novel compounds, which were subjected to molecular docking and molecular dynamics studies, and the results showed that the new compounds formed many robust interactions with residues within the active pocket and could maintain stable binding to the receptor proteins. This study not only provides a powerful screening tool for designing novel FAK inhibitors, but also presents a series of novel FAK inhibitors with high micromolar activity that can be used for further characterization. It provides a reference for addressing the shortcomings of drug metabolism and drug resistance of traditional FAK inhibitors, as well as the development of novel clinically applicable FAK inhibitors.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"3749-3765"},"PeriodicalIF":2.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139087029","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genetic variants and haplotype structures of miRNA host genes in cancer and obesity. 癌症和肥胖症中 miRNA 宿主基因的遗传变异和单倍型结构。

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-04-01 Epub Date: 2024-01-04 DOI: 10.1080/07391102.2023.2300056

Morteza Gholami

{"title":"Genetic variants and haplotype structures of miRNA host genes in cancer and obesity.","authors":"Morteza Gholami","doi":"10.1080/07391102.2023.2300056","DOIUrl":"10.1080/07391102.2023.2300056","url":null,"abstract":"Cancer and obesity are two important public health problems. This study aimed to investigate the role of genetic variants and haplotypes of miRNA host genes in cancer and obesity. Data from the catalog of genome-wide association studies (GWAS) were used to find significant variants (index). Then, 1000-genome phase 3 data were used to find haplotypic variants (proxy) associated with these diseases. The candidate variants and haplotypes were identified from proxy and index variants. Finally, SNP function analysis was performed. All GWAS-significant cancer-associated miRNA host gene variants, including MIR4713HG, MIR663AHG, MIR99AHG and MIR4435-2HG, were also significantly associated with obesity. The rs703764 variant was common between cutaneous melanoma and obesity traits in the European population (P ≤ 5E-8). The rs2414098 variant was associated with endometrial cancer (P ≤ 5E-13), and the rs7173595 variant was associated with waist-hip ratio (P ≤ 5E-13) and new CGGCATCA haplotypic located at MIR4713HG was identified in the European population. In addition, the ATCTTGTT haplotype for rs17041868 in MIR4435-2HG was identified to be associated with obesity traits (waist-hip ratio and BMI) in the European population (P ≤ 5E-8). This study found that rs703764 is a common genetic marker between cancer and obesity. The CGGCATCA haplotype is common between endometrial cancer and waist-hip ratio. Also, ATCTTGTT haplotype is associated with obesity traits. These results indicate that the variants and haplotypes of miRNAs host genes play an important role between cancer and obesity in the European population. It is suggested to investigate the effect of these structures in other populations.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"3645-3651"},"PeriodicalIF":2.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139087033","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

In silico identification and characterization of small molecule binding to the CD1d immunoreceptor. 小分子与 CD1d 免疫受体结合的硅学鉴定和特征描述。

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-04-01 Epub Date: 2023-12-18 DOI: 10.1080/07391102.2023.2294388

Prashanth Rathakrishnan, Andrew C McShan

{"title":"In silico identification and characterization of small molecule binding to the CD1d immunoreceptor.","authors":"Prashanth Rathakrishnan, Andrew C McShan","doi":"10.1080/07391102.2023.2294388","DOIUrl":"10.1080/07391102.2023.2294388","url":null,"abstract":"CD1 immunoreceptors are a non-classical major histocompatibility complex (MHC) that present antigens to T cells to elucidate immune responses against disease. The antigen repertoire of CD1 has been composed primarily of lipids until recently when CD1d-restricted T cells were shown to be activated by non-lipidic small molecules, such as phenyl pentamethyl dihydrobenzofuran sulfonate (PPBF) and related benzofuran sulfonates. To date structural insights into PPBF/CD1d interactions are lacking, so it is unknown whether small molecule and lipid antigens are presented and recognized through similar mechanisms. Furthermore, it is unknown whether CD1d can bind to and present a broader range of small molecule metabolites to T cells, acting out functions analogous to the MHC class I related protein MR1. Here, we perform in silico docking and molecular dynamics simulations to structurally characterize small molecule interactions with CD1d. PPBF was supported to be presented to T cell receptors through the CD1d F' pocket. Virtual screening of CD1d against more than 17,000 small molecules with diverse geometry and chemistry identified several novel scaffolds, including phytosterols, cholesterols, triterpenes, and carbazole alkaloids, that serve as candidate CD1d antigens. Protein-ligand interaction profiling revealed conserved residues in the CD1d F' pocket that similarly anchor small molecules and lipids. Our results suggest that CD1d could have the intrinsic ability to bind and present a broad range of small molecule metabolites to T cells to carry out its function beyond lipid antigen presentation.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"2929-2947"},"PeriodicalIF":2.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138803269","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Annonaceous acetogenins as promising DNA methylation inhibitors to prevent and treat leukemogenesis - an in silico approach. 茴香属植物炔苷元是一种很有前途的 DNA 甲基化抑制剂，可用于预防和治疗白血病的发生--这是在硅学方法中发现的。

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-04-01 Epub Date: 2023-12-27 DOI: 10.1080/07391102.2023.2297010

Udayadharshini Subaramaniyam, Divya Ramalingam, Ranjini Balan, Biswaranjan Paital, Pranati Sar, Nirmaladevi Ramalingam

{"title":"Annonaceous acetogenins as promising DNA methylation inhibitors to prevent and treat leukemogenesis - an in silico approach.","authors":"Udayadharshini Subaramaniyam, Divya Ramalingam, Ranjini Balan, Biswaranjan Paital, Pranati Sar, Nirmaladevi Ramalingam","doi":"10.1080/07391102.2023.2297010","DOIUrl":"10.1080/07391102.2023.2297010","url":null,"abstract":"Leukemia is a haematological malignancy affecting blood and bone marrow, ranking 10th among the other common cancers. DNA methylation is an epigenetic dysregulation that plays a critical role in leukemogenesis. DNA methyltransferases (DNMTs) such as DNMT1, DNMT3A and DNMT3B are the key enzymes catalysing DNA methylation. Inhibition of DNMT1 with secondary metabolites from medicinal plants helps reverse DNA methylation. The present study focuses on inhibiting DNMT1 protein (PDB ID: 3PTA) with annonaceous acetogenins through in-silico studies. The docking and molecular dynamic (MD) simulation study was carried out using Schrödinger Maestro and Desmond, respectively. These compounds' drug likeliness, ADMET properties and bioactivity scores were analysed. About 76 different acetogenins were chosen for this study, among which 17 showed the highest binding energy in the range of -8.312 to -10.266 kcal/mol. The compounds with the highest negative binding energy were found to be annohexocin (-10.266 kcal/mol), isoannonacinone (-10.209 kcal/mol) and annonacin (-9.839 kcal/mol). MD simulation results reveal that annonacin remains stable throughout the simulation time of 100 ns and also binds to the catalytic domain of DNMT1 protein. From the above results, it can be concluded that annonacin has the potential to inhibit the DNA methylation process and prevent leukemogenesis.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"3116-3129"},"PeriodicalIF":2.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139040036","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

An in silico investigation of the binding of flavones with CREB1 oncogene G-quadruplex DNA.

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-03-05 DOI: 10.1080/07391102.2025.2472391

Pallavi Agrawal, Maya S Nair

{"title":"An in silico investigation of the binding of flavones with CREB1 oncogene G-quadruplex DNA.","authors":"Pallavi Agrawal, Maya S Nair","doi":"10.1080/07391102.2025.2472391","DOIUrl":"https://doi.org/10.1080/07391102.2025.2472391","url":null,"abstract":"Stabilizing G-quadruplex structures through small molecule binding is an important area of research in cancer therapy. Cyclic AMP response element-binding protein 1 (CREB1) is a transcription factor of the CREB family that acts as an oncogene. It governs various roles in cellular processes, including the regulation of genes. CREB1 has guanine-rich regions which can form G-quadruplex (GQ) structures. Flavones are natural compounds with anticancer properties. We have investigated the binding mode and interaction mechanisms of three flavone compounds with the CREB1 GQ (CR-GQ) employing molecular docking and 100 ns molecular dynamics simulations, followed by an umbrella sampling method. The binding free energies estimated from MM-PBSA were -47.95, -107.55 and -98.28 kcal/mol, respectively, for flavone, baicalein and chrysin, showing that baicalein and chrysin bind with lower energy than flavone. Root mean square deviations and root mean square fluctuation values indicate that the GQ DNA-ligand system is stable throughout the simulations. The binding free energies and the estimated minimum values in the potential of mean force suggest that the binding reaction is energetically favourable. The compactness of the complexes is evident from the eigenvector map. Hydrogen bonds, pi-pi interactions and van der Waals interactions are the major driving forces in the complex formation. Among the three flavone compounds, baicalein and chrysin complexes are energetically more favourable than the flavone complex. The studied phytochemicals exhibit pharmacokinetic properties, suggesting their potential as promising drug candidates targeting CR-GQ. This study provides pragmatic data for discovering novel drugs targeting CR-GQ and extends the knowledge in stabilizing GQ structures using small molecules.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-14"},"PeriodicalIF":2.7,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143557095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Network pharmacological evaluation of Cressa cretica L.- an integrated approach of modern and ancient pharmacology. Cressa cretica L.的网络药理学评估--现代和古代药理学的综合方法。

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-03-04 DOI: 10.1080/07391102.2025.2472403

Pratham Gour Chintaluri, Aparna Ganapathy Vilasam Sreekala, Krishna Kant Gupta, Aparna Sivadasan, Vinod Kumar Nathan

{"title":"Network pharmacological evaluation of Cressa cretica L.- an integrated approach of modern and ancient pharmacology.","authors":"Pratham Gour Chintaluri, Aparna Ganapathy Vilasam Sreekala, Krishna Kant Gupta, Aparna Sivadasan, Vinod Kumar Nathan","doi":"10.1080/07391102.2025.2472403","DOIUrl":"https://doi.org/10.1080/07391102.2025.2472403","url":null,"abstract":"Cressa cretica L. is immensely valuable in pharmacology. Computational approach through network pharmacology has been attempted to understand lead molecules of Cressa and their interactions with multiple targets. The phytochemical components of methanolic extracts of Cressa leaves were identified using GC-MS analysis, revealing 16 compounds. Using the identified lead molecules, target proteins were predicted using SWISS-target prediction and were analyzed using Cytoscape. This led to the identification of 56 candidate protein targets, which were used to construct a network using CytoHubba, Centiscape, MCODE, and KEGG pathways. The STRING network was created using Cytoscape for analyzing protein-protein interactions, and the top 5 genes were chosen from a total of 12 algorithms in CytoHubba. The antioxidant effects of C. cretica were investigated using 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity, which showed an increase in the trend activity of the plant extract with an inhibition percentage of 51.53 ± 0.003%. This was further validated by ferric reducing antioxidant power (FRAP) assay that resulted in an antioxidant activity of 6.64 µg/mL at a high concentration of 500 µg/mL. Molecular docking and simulation were performed to study the interaction of human cyclooxygenase-2 (PDB ID: 5KIR) with Cressa metabolites. 5KIR exhibited a higher interaction with methyl stearate, forming two H-bond interactions with Arg 120 and Tyr 355. Molecular dynamics simulation analysis confirmed the stability of the protein-ligand complex. The network pharmacology analysis of putative proteins obtained from C. cretica revealed that the peroxisome proliferator-activated receptor gamma (PPARG) gene is found in numerous cancer pathways and can be inhibited.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-16"},"PeriodicalIF":2.7,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143542042","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0